• Journal of Life Science
• /
• v.23 no.4
• /
• pp.595-601
• /
• 2013

The clusters of orthologous groups of proteins (COG) algorithm was applied to identify essential proteins in eukaryotes and to measure the degree of conservation. Sixty-three orthologous groups, which were conserved in 66 microbial genomes, enlarged to 104 eukaryotic orthologous groups (KOGs) and 71 KOGs were conserved at the nuclear genome of 7 eucaryotes. Fifty-four of 71 translation-related genes were conserved, highlighting the importance of proteins in modern organisms. Translation initiation factors (KOG0343, KOG3271) and prolyl-tRNA synthetase (KOG4163) showed high conservation based on the distance value analysis. The genes of Caenorhabditis elegans appear to harbor high genetic variation because the genome showed the highest variation at 71 conserved proteins among 7 genomes. The 71 conserved genes will be valuable in basic and applied research, for example, targeting for antibiotic development.

• Korean Journal of Plant Taxonomy
• /
• v.38 no.1
• /
• pp.51-61
• /
• 2008

Leaves are indeterminate organs and possess a lot of genes which is involved in establishing leaf polarities. These polarities are regulated relatively early during leaf development and defined relative to the factors intrinsic to the primordia and interactions with the shoot apical meristem (SAM). Recently, several genes that control the polarity of lateral organs have been identified. Our genetic study of deformed root and leaf1 (drl1) mutant, which produces narrow, filament‐like leaves and defective meristems, revealed that DRL1 is involved in the regulation of SAM activity and leaf polarity. The DRL1 gene was found to encode a novel protein showing homology to Elongator‐associate protein (EAP) of yeast KTI12. The amino acid sequence of DRL1 is universally conserved in prokaryotes and eukaryotes. DRL1 and the plant DRL1 homologs clearly formed a monophyletic clade, suggesting the evolutionary conservation of DRL1 homologs was maintained in the genomes of all land plants.

• Korean Journal of Plant Resources
• /
• v.16 no.3
• /
• pp.257-263
• /
• 2003

The NDK1 is an ubiquitous enzyme that transfer phosphate groups from triphosphate nucleoside diphosphates(NDPs) in eukaryotes and prokaryotes. We isolated and characterized a cDNA encoding a nucleoside diphosphate kinase 1(CNDK 1) in Codonopsis lanceolata. The CNDK 1 is 444bp long and open reading frame of 447bp with a deduced amino acid of 148 residue. The CNDK 1 has an ATP binding site in 12­16 residue and phosphohistidine intermediate in 115 residue of amino acid sequence. Although several NDK 1 genes have been cloned in plants, but little is known about the functional significance of this enzyme during plant growth and development. The CNDK 1 shows the identities to Arabidopsis thaliana (71％), Oryza sativa(75％), Glycine max (79％), Brassica rapa (77％), Mesembryanthemum crystallinum (85 ％), Spinacia oleracea (83％), Pisum sativum (82％). The CNDK 1 of C. laceolata have a closer relationship of Glycine max and Pisum sativum at the phylogenic analysis.

• Journal of Life Science
• /
• v.13 no.6
• /
• pp.933-942
• /
• 2003

CoenzymeQ is a quinone derivative with a long isoprenoid side chain. It transports electrons in the respiratory chain located in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes. It also functions as an antioxidant. Saccharomyces cerevisine coq mutants, that are deficient coenzyme Q biosynthesis fail to aerobically grow. They are not able to grow on non-fermentable carbon sources, such as glycerol, either The putative $coq^{-7}$ gene involved in coenzyme Q biosynthesis of Neurospora crassa was cloned and used for complementation of S. cerevisiae coq7 mutant. The predicted amino acid sequence of N. crassa COQ7 showed about 58% homology with Coq7p of S. cerevisiae. The growth rate of S. cerevisiae $coq^7$ mutant transformed with the N. crassa $coq^{-7}$ gene was restored to the wild-type level. The complemented 5. cerevisiae strain was able to grow with glycerol as a sole carbon source and showed less sensitivities to linolenic acid, a polyunsaturated fatty acid.

• Journal of the Korean Applied Science and Technology
• /
• v.38 no.5
• /
• pp.1249-1254
• /
• 2021

UV induce oxidative stress and increase matrix metalloproteinase (MMP) expression, resulting in skin aging. Thus, preventing skin damage from ultraviolet B (UVB)-induced skin damage can attenuate skin aging. Spirulina is comprised of prokaryotes a powerful antioxidant. This study aimed to investigate the photoprotective effects of spirulina-derived phycocyanin (PC) against UVB radiation using human skin fibroblast. As a results, PC showed no toxicity at concentrations of 5-40 ㎍/mL in terms of fibroblast viability. Survival rate of UVB-irradiated fibroblast incresased to 73.5% from 50.5% with PC treatment. UVB treatment increased MMP-1 and MMP-9 expression whereas PC treatment decreased it. The results indicate that PC might reduce or prevent skin aging by reducing UVB irradiation-induced skin wrinkles and free radicals.

• BMB Reports
• /
• v.54 no.2
• /
• pp.98-105
• /
• 2021

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a family of DNA sequences originally discovered as a type of acquired immunity in prokaryotes such as bacteria and archaea. In many CRISPR systems, the functional ribonucleoproteins (RNPs) are composed of CRISPR protein and guide RNAs. They selectively bind and cleave specific target DNAs or RNAs, based on sequences complementary to the guide RNA. The specific targeted cleavage of the nucleic acids by CRISPR has been broadly utilized in genome editing methods. In the process of genome editing of eukaryotic cells, CRISPR-mediated DNA double-strand breaks (DSB) at specific genomic loci activate the endogenous DNA repair systems and induce mutations at the target sites with high efficiencies. Two of the major endogenous DNA repair machineries are non-homologous end joining (NHEJ) and homology-directed repair (HDR). In case of DSB, the two repair pathways operate in competition, resulting in several possible outcomes including deletions, insertions, and substitutions. Due to the inherent stochasticity of DSB-based genome editing methods, it was difficult to achieve defined single-base changes without unanticipated random mutation patterns. In order to overcome the heterogeneity in DSB-mediated genome editing, novel methods have been developed to incorporate precise single-base level changes without inducing DSB. The approaches utilized catalytically compromised CRISPR in conjunction with base-modifying enzymes and DNA polymerases, to accomplish highly efficient and precise genome editing of single and multiple bases. In this review, we introduce some of the advances in single-base level CRISPR genome editing methods and their applications.

• Genomics & Informatics
• /
• v.20 no.3
• /
• pp.35.1-35.9
• /
• 2022

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

• Journal of Microbiology and Biotechnology
• /
• v.31 no.7
• /
• pp.912-920
• /
• 2021

SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.

• Journal of Species Research
• /
• v.12 no.spc2
• /
• pp.45-53
• /
• 2023

In July 2018, solar saltern samples were collected from Siheung, Gyeonggi-do Province to obtain unrecorded haloarchaea in Korea. The samples were suspended in a 20% NaCl (w/v) solution, and serial dilution was performed in fresh DB Characterization media No. 2. The strains isolated in this study showed at least 98.7% sequence similarity or more compared to the previously reported. Finally, 16 haloarchaeal strains, which were not reported in Korea but validly published under the International Code of Nomenclature of Prokaryotes (ICNP), were obtained from a solar saltern in Siheung. These 16 isolates were allocated to the orders Halobacteriales and Haloferacales. The 10 Halobacteriales strains were classified into the family Halobacteriaceae and Haloarculaceae. Each family belonged to three genera, respectively. The other six Haloferacales belonged to the families Haloferacaceae and Halorubraceae. Each family belonged to genus genus, respectively. Collectively, the unrecorded haloarchaeal strains belonged to two orders, four families, and eight genera. During the research, the possibility of discovering previously unknown species in domestic solar saltern was established. Gram-staining, cell morphology, physiological and basic biochemical parameters, and phylogenetic analysis were all performed in this study and are described in detail for each strain.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.48 no.1
• /
• pp.42-47
• /
• 2024

The value of silkworms as functional health food materials has increased, as has the interest in its disease control for stable production, and in the economic value of entomopathogenic microorganisms. In this study, we isolated and identified disease-causing fungi from white muscardine silkworms, and confirmed whether this strain could produce white muscardine silkworms. For the analysis of the cause of white muscardine disease in the infected silkworms, the fungi and prokaryotes causing the disease were identified, isolated, and identified using metagenome analysis. Metagenomic analysis detected a large amount of the fungus Metarhizium rileyi in silkworms, and a large amount of the bacterium Enterococcus mundtii, which was presumed to be the causative agent of the disease. For accurate identification of the fungi, these were purified by culture medium, and sequencing and phylogenetic tree analyses were performed using an internal transcribed spacer. As a result, M. rileyi, Cladosporium cladosporioides, and C. tenuissimum were identified. In general, M. rileyi is known to form green conidia, but in this study, white-yellow conidia were formed, indicating that the exact causative agent of the fungal disease cannot be estimated by diagnosing the symptoms. Thus, a diagnostic method is necessary for the continuously collection of required pathogens, and identifying their morphological and genetic characteristics.